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PPIX

PPIX (protoporphyrin IX) is a natural tetrapyrrole compound that serves as a precursor to heme, the iron-containing cofactor of hemoglobin and other important proteins.
It is an intermediate in the biosynthetic pathway of heme, playing a critical role in cellular respiration and oxygen transport.
PPIX can also accumulate in certain medical conditions, leading to photosensitivity and other clinical manifestations.
Researchers studying PPIX and its physiological functions may find it useful to consult the liteature and optimize their experimental protocols using AI-driven tools like PubCompare.ai to enhance the reproducibility and accuracy of their findings.

Most cited protocols related to «PPIX»

For analysis of PpIX levels, tumors were harvested, embedded for frozen sectioning, and analyzed on a Leica confocal microscope as described (15 (link)). Standard hematoxylin-and-eosin staining was done on formalin-fixed/paraffin-embedded tissues, and immunohistochemical staining was performed as described (23 (link)). Sources and dilutions of antibodies were: Active caspase-3 (BioVision, Mountain View CA; 1:50), ferrochelatase FC (1:100), E-Cad (Santa Cruz Biotechnology, 1:100), Ki67 (NeoMarkers, Fremont, CA; 1:250), GAPDH (Santa Cruz Biotechnology; 1:100), TNFα (BioXcell, 1:100), CY3 or FITC-conjugated Donkey anti-rabbit (Jackson ImmunoResearch; 1:1500). To assess cell proliferation in vivo, EdU (5-ethynyl-2’-deoxyuridine) was injected (100 µg /mouse, i.p.) 1 hour prior to sacrifice. Formalin fixed tissues were sectioned and incubated with the Click-iT® reaction cocktail per manufacturer's instructions (Invitrogen, Carlsbad, CA). To estimate cell death, the TUNEL assay was performed on paraffin sections as directed by the manufacturer (Roche Applied Science, Indianapolis, IN).
Publication 2011
5-ethynyl-2'-deoxyuridine Antibodies Biological Assay Caspase 3 Cell Death Cell Proliferation Eosin Equus asinus Ferrochelatase Fluorescein-5-isothiocyanate Formalin GAPDH protein, human Hematoxylin In Situ Nick-End Labeling Microscopy, Confocal Mus Neoplasms Paraffin Paraffin Embedding PPIX Rabbits Technique, Dilution Tissues Tumor Necrosis Factor-alpha
PpIX-specific fluorescence was analyzed by fluorescence microscopy on a confocal laser scanning microscope (Leica Microscopy Systems GmbH, Wetzlar, Germany). Cells, plated on sterile microscope coverslips in 35 mm dishes at 50,000 cells/dish, were conditioned with MTX or control media as above. PpIX-specific fluorescence in the living cells was collected on the confocal microscope (excitation 488 nm, emission 550–700 nm) and the digital images analyzed using IPLab image processing software (Signal Analytics, Vienna, VA). The background signal threshold was set to reveal only specific (mitochondrial) PpIX fluorescence in controls. This setting was then applied to all images within the same series. Total integrated area was calculated and divided by number of cells in the field (counted in corresponding phase-contrast images). PpIX levels were expressed as arbitrary fluorescence units (total pixels) per cell. In other experiments described below, frozen tissue sections from organotypic tissues, from chemically-induced mouse skin tumors, or from subcutaneous A431 tumors in nude mice, were analyzed by confocal imaging as follows. Cryosections (10 μ) were placed on glass slides, briefly air dried, coverslipped with Vectashield (Vector laboratories, Burlingame, CA), and viewed on the confocal microscope with a 40x lens under oil using excitation at 633 nm and image collection in the red channel (emission 650–780 nm).
Publication 2009
Cells Cloning Vectors Cryoultramicrotomy Fluorescence Frozen Sections Hyperostosis, Diffuse Idiopathic Skeletal Lens, Crystalline Mice, Nude Microscopy Microscopy, Confocal Microscopy, Confocal, Laser Scanning Microscopy, Fluorescence Microscopy, Phase-Contrast Mitochondria Mus Neoplasms PPIX Skin Neoplasms Sterility, Reproductive Tissues
Analysis of siderophore, PpIX and free amino acids was carried out by reversed phase HPLC as described previously [20] (link), [43] (link), [46] (link). To quantify extracellular or intracellular siderophores, culture supernatants or cellular extracts were saturated with FeSO4 and siderophores were extracted with 0.2 volumes of phenol. The phenol phase was separated and subsequent to addition of 5 volumes of diethylether and 1 volume of water, the siderophore concentration of the aqueous phase was measured photometrically using a molar extinction factor of 2996/440nm (M−1cm−1).
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Publication 2010
A-factor (Streptomyces) Amino Acids Cell Extracts Ethyl Ether Extinction, Psychological factor A High-Performance Liquid Chromatographies Molar Phenol PPIX Protoplasm Siderophores
All glioma resections were performed with navigational guidance (Stealth Station Cranial Treon or S7; Medtronic, CO, USA) using T1-contrast-enhanced MRI co-registered with PETmax or CSImax as described elsewhere [11] , [17] (link). Depending on tumor location, additional functional imaging data from fMRI and DTI were used as appropriate. The following protocol was applied for tissue sampling and assessment of potential PpIX fluorescence during each glioma resection:
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Publication 2013
Cranium Fluorescence fMRI Glioma Neoplasms by Site PPIX Tissues
We used a fiberoptic probe connected to a spectrometer to measure the response of brain tissue excited with blue light (wavelength: λ = 405 nm) followed by interrogation with broadband white light (λ = 450–720 nm) delivered through the fiberoptic probe tip to compensate for signal losses due to light absorption and scattering by the tissue using novel light-transport modeling methods.7 (link) The relative contributions of oxyhemoglobin and deoxyhemoglobin to the total light absorption were determined in situ by using the measured white-light reflectance spectrum fitted to a diffusion model of the reflectance where the intrinsic absorption spectra of each of these proteins were assumed to be known.
A mathematical model7 (link) (Appendix) was then used to quantify the absolute concentration of PpIX based on the measured fluorescence spectrum. Since the fluorescence measurements are distorted by variations in tissue optical properties, quantitative determination of the concentration of fluorescing molecules requires knowledge of the absorption and scattering spectra of the tissue being sampled. Moreover, PpIX is not the only molecule contributing to the measured fluorescence spectrum (other contributors include tissue autofluorescence and photoproducts such as photoprotoporphyrin resulting from PpIX photobleaching3 (link)). However, the spectral shapes of the primary fluorophores of interest are known, which allows spectral decomposition to be used to determine their relative contributions, and in the case of PpIX, the absolute concentration (CPpIX). By incorporating these light-transport modeling methods that eliminate the distorting effects of variations in tissue optical properties and account for the presence of multiple fluorescent species, quantitative measurements of CPpIX can be obtained intraoperatively and in vivo with an unprecedented degree of sensitivity and fidelity.
Publication 2011
Brain deoxyhemoglobin Diffusion Fluorescence Hypersensitivity Light Oxyhemoglobin PPIX Proteins Tissues

Most recents protocols related to «PPIX»

Experiments with pig brains were permitted by the Health and Veterinary Office Münster (Reg.-No. 05 515 1052 21). Pig brain was obtained from a local butcher and separated into the following anatomical parcels: cerebrum, cerebellum, hypothalamus, and brain stem/spinal cord. Each tissue section was washed with distilled water, roughly cut into 10 × 10 × 10 mm pieces and homogenized using a blender (VDI 12, VWR International, Hannover, Germany). Homogenates were stored at − 20 °C. For adjustment of pH to 5–9, 0.5 M tris(hydroxymethyl)aminomethane (Tris-base, Serva, Heidelberg, Germany) buffer was prepared with hydrochloric acid (HCl, Honeywell Riedel–de Haen, Seelze, Germany). Reference tissue homogenates (RTHs) with controlled pH (pH-RTHs) were composed of RTHs and buffer (w/v), as displayed in supplementary Table S1 before spiking of PPIX. For the preparation of RTHs without pH control (pH ~ 7), 200 to 600 mg of the homogenates were directly spiked with PPIX (Enzo Life Sciences GmbH, Lörrach, Germany) stock solution (300 pmol/µl in dimethyl sulfoxide, Merck KGaA, Darmstadt, Germany) to the desired concentrations (0.0, 0.5, 0.75, 1.0, 2.0, 3.0 and 4.0 pmol/mg) and homogenized using a vortex mixer. RTHs and pH-RTHs were transferred to a Petri dish forming tissue samples of about 4 × 4 × 2 mm. Hyperspectral measurements were performed immediately using the same parameters as for tissue biopsies. The software calculated the PPIX contribution in µg/ml based on the calibration with liquid phantoms18 (link)–20 (link),25 (link)–28 (link). A unit related to the sample weight is superior and more common in solid tissue samples like homogenates or brain biopsies, because these samples are routinely weighed for analysis in the laboratory. Thus, we refer to pmol/mg for the spiked samples of homogenates experiments and evaluate them in relation to the calculated PPIX contribution from HI in µg/ml. All generated raw data analyzed during this study are included in the supplementary data file.
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Publication 2023
Biopsy Brain Brain Stem Buffers Cerebellum Cerebrum Hydrochloric acid Hyperostosis, Diffuse Idiopathic Skeletal Hypothalamus methylamine PPIX Spinal Cord Sulfoxide, Dimethyl Tissues Tromethamine
The commercially available surgical microscope KINEVO 900 equipped with the BLUE 400 filter system (Carl Zeiss Meditec (CZM) AG, Oberkochen, Germany) was used in the operating theatre to visualize PPIX fluorescence in vivo.
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Publication 2023
Fluorescence Microscopy Operative Surgical Procedures PPIX
The strains used in this study are summarized in Additional file 1: Table S1. Molecular cloning and manipulation of plasmids were performed using E. coli DH5α. The plasmids and oligonucleotides used in this work are listed in Additional file 2: Tables S2 and Additional file 3: Table S3. For PPIX and heme fermentation, E. coli strain BL21 and MR-Fe20 medium were used. MR-Fe20 medium contained 6.67 g/L KH2PO4, 4 g/L (NH4)2HPO4, 0.8 g/L MgSO4∙7H2O, 0.8 g/L citric acid, 20 mg/L FeSO4∙7H2O, and 5 mL of trace metal solution A per liter. Trace metal solution A contained 0.5 mol of HCl, 2 g/L CaCl2, 2.2 g/L ZnSO4∙7H2O, 0.5 g/L MnSO4∙4H2O, 1 g/L CuSO4∙5H2O, 0.1 g/L (NH4)6Mo7O24∙4H2O, 0.02 g/L Na2B4O7∙10H2O, and 10 g/L FeSO4∙7H2O [25 (link)] (Additional file 4: Table S4).
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Publication 2023
Citric Acid Escherichia coli Fermentation Heme Metals Oligonucleotides Plasmids PPIX Strains Sulfate, Magnesium
The free base of protoporphyrin IX H2PP-IX was from Sigma-Aldrich (Burlington, MA, USA) and the free base of chlorin-e6 was from the Russian Technological University RTU MIREA. The structure and purity of the compounds were confirmed by NMR, UV/Vis spectroscopy and luminescent spectroscopy.
For the synthesis of Cu (II) protoporphyrin (Cu-PP-IX), 15 mg of the free base of protoporphyrin IX was dissolved in 25 mL of methylene chloride and a solution of 8 mg of Cu (II) acetate in 20 mL of ethanol was added to the resulting solution. The solutions were mixed, and the resulting solution was stirred at 40 °C for 30 min. The solvents were removed in a vacuum and the product was dissolved in methylene chloride and purified by column chromatography from traces of the original protoporphyrin IX. The yield of Cu-PP-IX was 16 mg (98%). The structure of the resulting Cu-PP-IX compound was confirmed by MALDI TOF mass spectrometry and UV/Vis spectroscopy in a chlorobenzene solution.
For the synthesis of Cu (II) chlorin-e6 (Cu-C-e6), 15 mg of the free base of chlorin-e6 was dissolved in 30 mL of methylene chloride and a solution of 7 mg of Cu (II) acetate in 20 mL of ethanol was added to the resulting solution. The solutions were mixed and the resulting solution was stirred at 35 °C for 40 min. The solvents were removed in a vacuum. The product was dissolved in methylene chloride and purified by column chromatography from traces of the original chorine e6, and the solvent was removed in vacuum. The yield of Cu-C-e6 was 16 mg (97%). The structure of the resulting Cu-C-e6 compound was confirmed by MALDI TOF mass spectrometry and UV/Vis spectroscopy in a chlorobenzene solution.
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Publication 2023
Acetate Anabolism chlorobenzene Chromatography Ethanol Luminescence magnesium protoporphyrin Mass Spectrometry Methylene Chloride phytochlorin PPIX protoporphyrin IX Solvents Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Spectrum Analysis Vacuum
Induction of anesthesia was performed by the attending anesthesiologist. Intraoperative monitoring, ECG-based heart rate, invasive blood pressure, body temperature, skin temperature and oxygen saturation, inspired oxygen fraction (FiO2), anesthesia infusion rate and vasopressor pump setting were part of the standard monitoring and were stored in the electronic patient data management system. All patients were kept normothermic with use of a warm air blanket. Normovolemia was pursued with intravenous crystalloids based on the pulse pressure variation index (threshold above 13).
MitoPO2 measurements were performed through the use of the COMET® monitor (Photonics Healthcare, Utrecht, the Netherlands). In order to upregulate PpIX, a self-adhesive patch containing 8mg 5-aminolevulinc acid (ALA) (Alacare®, photonamic GmbH und Co. KG, Pinneberg, Germany) was applied on the sternal skin. Alacare ® is used off-label for mitochondrial oxygen tension measurements. To enhance ALA penetration adequate skin preparation proved essential. Hair was shaved (if present) and the skin was rubbed with a fine abrasive pad to remove the top parts of the stratum corneum. During ALA application, the skin was protected from light. Application of at least 5 hours allowed for a suitable concentration of PpIX to be synthesized in order to enable measurements of mitoPO2. For the logistical reason that the surgeries often started at 8 a.m. and it was not considered patient-friendly to place the plaster in the middle of the night, longer application times were accepted. After the induction of anesthesia, the ALA patch was removed and the measuring probe applied to the ALA-treated skin. The mitoPO2 was automatically measured every 5 minutes during the operation.
In addition to the mitoPO2, tissue oxygenation saturation and perfusion parameters were measured intraoperatively using the O2C (oxygen to see version 2424, Lea Medizintechnik GmbH, Giessen, Germany). The O2C measures three parameters: The local capillary venous saturation (StO2), the local velocity of blood given in velocity units (VU) and the local microvascular blood flow given in flow units (AU). Both the COMET® Skin Sensor and the O2C probe (LFX-43) were positioned on the sternum next to each other.
All measurements were performed from the start of surgery until the end of surgery, in order to exclude the effects of induction of anesthesia and the accompanying influences of medication and pre-oxygenation on mitochondrial and microvascular parameters. To observe the feasibility and stability of the mitoPO2 measurements the outcome measures included: mitoPO2 (mmHg), local capillary venous saturation (%), flow (AU), inspired oxygen fraction (FiO2, %), peripheral oxygen saturation (SpO2, %) and skin temperature (degrees Celsius).
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Publication 2023
Acids Anesthesia Anesthesiologist Anesthetic Effect BLOOD Blood Pressure Body Temperature Capillaries Cell Respiration Comet Assay Hair Light Microcirculation Mitochondria Operative Surgical Procedures Oxygen Oxygen Saturation Patients Perfusion Pharmaceutical Preparations PPIX Pulse Pressure Rate, Heart Regional Blood Flow Saturation of Peripheral Oxygen Skin Skin Temperature Solutions, Crystalloid Sternum Tissues Vasoconstrictor Agents Veins

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5-ALA is a chemical compound used in laboratory settings. It is a precursor in the biosynthesis of heme, a critical component of hemoglobin and other important biological molecules. 5-ALA is commonly used in various scientific applications, such as cell and tissue studies, without making claims about its intended use.
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More about "PPIX"

Protoporphyrin IX (PPIX) is a critical compound in the heme biosynthetic pathway, serving as a precursor to the iron-containing cofactor found in hemoglobin and other vital proteins.
This tetrapyrrole molecule plays a crucial role in cellular respiration and oxygen transport.
PPIX accumulation can occur in certain medical conditions, leading to photosensitivity and other clinical manifestations.
Researchers studying PPIX and its physiological functions may find it useful to consult the literature and optimize their experimental protocols using AI-driven tools like PubCompare.ai.
This platform can help enhance the reproducibility and accuracy of their findings by allowing them to easily locate protocols from literature, preprints, and patents, and use AI-driven comparisons to identify the best protocols and products for their research needs.
PPIX is closely related to other important compounds and technologies, such as 5-ALA (5-aminolevulinic acid), which can be used to detect and treat certain types of cancer by inducing PPIX accumulation.
Fluorescence-based instruments like the FACSCalibur flow cytometer, Synergy Mx Fluorescence plate reader, Infinite M200 Pro, and Fluoromax-3 fluorescence spectrometer can be used to study PPIX and its properties.
The solvent DMSO (dimethyl sulfoxide) is often used in PPIX-related research, and palmitic acid is a fatty acid that can influence PPIX biosynthesis.
Additionally, the U-LH100HG and P8293 are products that may be relevant to PPIX research and clinical applications.